1-236021631-T-C

Position:

• chr1-236021631-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002508.3(NID1):​c.2128+2439A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,894 control chromosomes in the GnomAD database, including 28,360 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.60 (28360 hom., cov: 31)
• Consequence: NID1 NM_002508.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

Genes affected

NID1 (HGNC:7821): (nidogen 1) This gene encodes a member of the nidogen family of basement membrane glycoproteins. The protein interacts with several other components of basement membranes, and may play a role in cell interactions with the extracellular matrix. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NID1	NM_002508.3	c.2128+2439A>G		intron_variant		ENST00000264187.7	NP_002499.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NID1	ENST00000264187.7	c.2128+2439A>G		intron_variant		1	NM_002508.3	ENSP00000264187.6
NID1	ENST00000366595.7	c.2128+2439A>G		intron_variant		1		ENSP00000355554.3

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90903 AN: 151776 Hom.: 28320 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.561

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.599 AC: 91001 AN: 151894 Hom.: 28360 Cov.: 31 AF XY: 0.603 AC XY: 44782 AN XY: 74232

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.560

Alfa AF: 0.534 Hom.: 11435

Bravo AF: 0.605

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.092
DANN	Benign	0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10754833; hg19: chr1-236184931; COSMIC: COSV51617286;